This special issue examines the role of agencies and agency-like bodies in the EU's Area of Freedom, Security and Justice (AFSJ) – an umbrella term for police and judicial cooperation, border management, asylum and migration, and counter-terrorism – which have acquired increasing importance in the governance of the EU. This introduction reviews the existing literature and sets the scene for the research articles that are included in this special issue. It also argues that future scholarship on these AFSJ agencies would significantly gain by being developed along two research tracks. The first of these would investigate the forces that have led to the creation of these AFSJ agencies in the first place, especially because understanding these factors can shed significant light on where these agencies might be heading in future. The second research track would examine how ‘legitimate’ each of these agencies is, as part of a would-be democratic polity at the EU level.